Open Database Searching Enables the Identification and Comparison of Bacterial Glycoproteomes without Defining Glycan Compositions Prior to Searching

1. Download : Download high-res image (118KB)
2. Download : Download full-size image

Highlights

• •We demonstrate the use of open searching for the detection of atypical glycosylation in bacterial glycoproteomes.
• •We show that although open searching is able to detect unique glycoforms it is less sensitive for the detection of multiply glycosylated peptides than focused searches.
• •Using open search delta mass profiles, we demonstrate glycan use across bacterial glycoproteomes can be easily compared.
• •For the Burkholderia genus we confirm the use of similar glycans for protein glycosylation yet also highlight that species specific glycans do exist.

     

A comparative study of the ori sequences from the mitochondrial genomes of twenty wild-type yeast strains

The ori sequences of the mitochondrial genomes of 20 wild-type strains of Saccharomyces cerevisiae were compared with those of the previously studied strain A (de Zamaroczy et al., 1984). The seven canonical ori sequences of this strain appear to be present in all strains tested, but in most strains ori1 is replaced by an extensively rearranged ori1 ¹ sequence, and an additional ori sequence, ori8, is present between the oxi3 and the 15S RNA genes; one strain, B, lacks ori4. The location and orientation of ori sequences of three strains, B, C and K, were found to be the same as in strain A. The primary structures of four ori sequences from three different strains (ori1 of strain J69-1B, ori3 and ori5 of strain K, ori6 of strain D273-10B) were found to be identical with the corresponding ori sequences previously investigated. Hybridization experiments with different on probes indicated a conservation of ori2–ori7 sequences in all strains tested. The primary structure of a petite genome derived from strain B and carrying ori1 ¹ is reported and discussed.     

Isolation and expression analysis of proline metabolism-related genes in Chrysanthemum lavandulifolium

Proline plays a significant role in plant resistance to abiotic stresses, and its level is determined by a combination of synthesis, catabolism and transport. The primary proteins involved are Δ¹-pyrroline-5-carboxylate synthetase (P5CS), proline dehydrogenase (PDH) and proline transporter (ProT). To utilise proline metabolism to improve the stress resistance of Chrysanthemum × morifolium, we isolated two P5CS-homologous genes (ClP5CS1 and ClP5CS2), one PDH gene (ClPDH) and four ProT-homologous genes (ClProT1-4) (GenBANK accession numbers: KF743136–KF743142) from Chrysanthemum lavandulifolium, which is closely related to chrysanthemums and exhibits strong resistance to stresses. Expression analysis of these genes in different organs and under various stresses indicated that ClP5CSs showed substantial constitutive expression, while ClPDH was only strongly expressed in the capitulum and was inhibited under most stresses. The expression patterns of four ClProT genes presented characteristics of organ specificity and disparity under stresses. Above all, the expression of ClProT2 was restricted to above-ground organs, especially strong in the capitulum and could be obviously induced by various stress conditions. Promoters of ClPDH and ClProTs contained many cis-acting regulatory elements involved in stress responses and plant growth and development. High levels of free proline were found in flower buds, the capitulum under the non-stress condition and later periods of stress conditions except cold treatment. Interestingly, organ specificity and disparity also exist in the level of free proline under different stress conditions. Our study indicates that ClProTs play significant roles in proline accumulation and stress responses, and that ClProT2 could be used to genetically modify the stress resistance of chrysanthemums. In addition, proline metabolism might be closely related to plant flowering and floral development.     

Identification and characterization of Tube in the Chinese mitten crab Eriocheir sinensis

As a key component of the Toll signaling pathway, Tube plays central roles in many biological activities, such as survival, development and innate immunity. Tube has been found in shrimps, but has not yet been reported in the crustacean, Eriocheir sinensis. In this study, we cloned the full-length cDNA of the adaptor Tube for the first time from E. sinensis and designated the gene as EsTube. The full-length cDNA of EsTube was 2247-bp with a 1539-bp open reading frame (ORF) encoding a 512-amino acid protein. The protein contained a 116-residue death domain (DD) at its N-terminus and a 272-residue serine/threonine-protein kinase domain (S_TKc) at its C-terminus. Phylogenetic analysis clustered EsTube initially in one group with other invertebrate Tube and Tube-like proteins, and then with the vertebrate IRAK-4 proteins, finally with other invertebrate Pelle proteins. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis results showed that EsTube was highly expressed in the ovary and testis, and moderately expressed in the thoracic ganglia and stomach. EsTube was expressed at all selected stages and was highly expressed in the spermatid stage (October, testis) and the stage III-2 (November, ovary). EsTube was differentially induced after injection of lipopolysaccharides (LPS), peptidoglycan (PG) or zymosan (β-1,3-glucan). Our study indicated that EsTube might possess multiple functions in immunity and development in E. sinensis.